Contacts of the strand formed by residues 157 - 169 (chain B) in PDB entry 5CVE
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 157 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127B ASP* 4.1 9.7 + - - +
129B TYR 3.4 12.6 - - - +
130B ASP 4.5 0.4 - - - +
132B ILE* 3.6 22.7 - - + -
153B CYS 3.6 9.2 - - - +
154B LYS* 3.4 19.4 + - + +
155B GLY 5.0 1.2 - - - +
156B SER* 1.3 79.2 - - - +
158B ARG* 1.3 69.5 + - - +
159B PRO* 4.7 0.2 - - - +
161B GLY* 3.7 18.8 - - - +
162B ILE* 3.6 28.7 - - - +
163B ILE* 4.1 22.2 - - + +
223B ARG* 4.7 12.3 - - + +
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Residues in contact with ARG 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B SER* 3.7 20.6 + - - -
64B CYS* 4.9 3.8 - - - +
112B ARG* 5.2 7.7 - - - +
127B ASP* 2.9 42.2 + - - +
128B SER* 3.5 18.2 + - - +
129B TYR 2.9 28.6 + - - +
130B ASP* 3.5 22.4 - - - +
157B LEU* 1.3 78.7 - - - +
159B PRO* 1.3 77.6 - - + +
160B ASN 3.3 0.5 + - - -
161B GLY* 2.9 14.0 + - - -
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Residues in contact with PRO 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B LYS 4.7 1.0 - - - +
61B GLY 5.0 2.9 + - - -
127B ASP* 3.7 13.0 - - - +
130B ASP* 4.7 4.2 - - - +
157B LEU 4.7 0.2 - - - +
158B ARG* 1.3 95.0 - - + +
160B ASN* 1.3 71.0 + - - +
161B GLY* 3.2 4.2 + - - -
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Residues in contact with ASN 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B GLY 5.3 0.2 + - - -
57B PRO 3.6 9.0 + - - +
58B ASN* 3.3 34.8 - - - +
59B LYS* 3.0 28.8 + - - +
60B THR* 2.8 27.3 + - - -
158B ARG 3.3 0.4 + - - -
159B PRO* 1.3 75.9 + - - +
161B GLY* 1.3 64.3 + - - +
223B ARG* 3.2 19.9 + - - +
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Residues in contact with GLY 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B THR* 4.4 0.7 - - - -
61B GLY 5.9 0.2 - - - -
130B ASP* 3.1 22.4 - - - -
157B LEU* 3.7 14.9 - - - +
158B ARG 2.9 17.7 + - - -
159B PRO 3.1 2.5 + - - -
160B ASN* 1.3 83.3 - - - +
162B ILE* 1.3 59.7 + - - -
223B ARG* 3.2 23.4 + - - +
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Residues in contact with ILE 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B LEU* 3.9 12.6 - - + -
52B PHE* 3.8 36.3 - - + -
60B THR* 3.9 8.3 - - - +
130B ASP 2.9 7.0 + - - +
131B VAL* 3.3 18.0 - - + -
132B ILE 3.0 23.4 + - - +
157B LEU* 3.6 6.5 - - - +
161B GLY* 1.3 79.5 - - - +
163B ILE* 1.3 64.0 + - - +
164B VAL* 3.9 23.3 - - + -
202B LEU* 3.7 18.8 - - + -
221B ALA* 4.6 2.5 - - + -
222B LEU 3.3 9.4 - - - +
223B ARG* 3.4 22.7 - - - +
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Residues in contact with ILE 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ILE* 3.3 19.3 - - + +
134B ILE* 3.7 28.0 - - + -
150B LEU* 4.4 4.7 - - + -
153B CYS* 3.7 23.8 - - + -
154B LYS* 3.8 15.7 - - - +
157B LEU* 4.1 11.0 - - + -
162B ILE* 1.3 75.4 - - - +
164B VAL* 1.3 67.2 + - - +
165B ILE* 4.5 0.9 - - + -
199B LEU* 3.8 31.4 - - + -
220B PHE 3.6 0.5 - - - +
221B ALA* 3.5 1.4 - - - -
222B LEU* 2.7 56.2 + - + +
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Residues in contact with VAL 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B PHE* 4.1 17.5 - - + -
49B LEU* 4.4 3.4 - - + -
131B VAL* 4.8 2.2 - - + -
132B ILE 2.8 11.2 + - - +
133B TRP* 3.6 50.5 - - + -
134B ILE* 2.8 30.1 + - - +
162B ILE* 3.9 24.7 - - + -
163B ILE* 1.3 78.6 - - - +
165B ILE* 1.3 71.8 + - - +
166B LYS 4.5 0.2 - - - +
219B SER* 4.8 3.1 - - - -
220B PHE 3.2 10.8 - - - +
221B ALA* 4.3 5.4 - - - -
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Residues in contact with ILE 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B ILE* 3.3 20.9 - - + +
138B ILE* 4.0 37.0 - - + -
146B LEU* 5.6 1.1 - - + -
150B LEU* 4.1 25.8 - - + -
163B ILE* 4.2 1.1 + - + -
164B VAL* 1.3 75.9 - - - +
166B LYS* 1.3 67.5 + - - +
167B ASP* 4.4 3.1 - - + -
169B MET* 5.0 0.4 - - + -
190B VAL* 5.1 5.2 - - + -
194B ILE* 4.2 13.0 - - + -
219B SER* 3.2 2.1 - - - -
220B PHE* 2.7 56.1 + - + +
222B LEU* 3.9 25.1 - - + -
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Residues in contact with LYS 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ASP* 2.8 26.3 + - - -
44B SER* 4.1 1.2 - - - -
45B SER* 2.9 29.0 + - - +
133B TRP* 4.4 11.0 - - + +
134B ILE 2.9 8.1 + - - -
135B GLN* 3.1 32.5 - - + +
136B TRP* 3.0 24.4 + - - -
164B VAL* 4.1 1.3 - - + -
165B ILE* 1.3 73.9 - - - +
167B ASP* 1.3 63.1 + - - +
207B GLN* 2.7 31.7 + - - -
217B VAL* 4.0 18.2 - - + -
218B TYR 3.2 5.8 - - - +
219B SER* 3.2 26.3 + - - +
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Residues in contact with ASP 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B GLN* 4.1 0.5 - - - -
136B TRP* 3.1 29.5 + - - +
137B VAL 2.9 24.9 + - - -
138B ILE* 3.1 32.3 + - + +
139B GLY 4.9 2.8 + - - -
165B ILE* 4.2 3.3 - - + -
166B LYS* 1.3 73.3 - - - +
168B ASN* 1.3 85.6 + - - +
169B MET* 3.6 17.9 + - + +
217B VAL* 3.3 6.6 - - - +
218B TYR 3.0 31.2 + - - +
1E PBE 4.7 1.9 - - - -
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Residues in contact with ASN 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B TRP* 2.9 23.8 + - - +
138B ILE* 5.4 1.6 - - - +
167B ASP* 1.3 86.7 + - - +
169B MET* 1.3 69.7 + - - +
184B CYS* 3.8 22.6 - - + +
185B ARG 4.2 4.0 + - - +
215B TYR* 3.9 14.6 - - + +
216B HIS 3.4 6.1 - - - -
217B VAL* 3.6 10.8 - - - +
1E PBE 2.8 32.1 + - - -
2E PRO* 3.8 8.2 - - - +
3E LYS* 4.0 16.6 - - - +
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Residues in contact with MET 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B ILE* 4.4 7.0 - - + -
165B ILE* 5.0 0.9 - - + -
167B ASP* 3.7 26.7 - - + +
168B ASN* 1.3 88.4 - - - +
170B ALA* 1.3 67.8 + - - +
171B GLN* 4.0 2.7 + - - +
184B CYS* 3.5 3.4 - - - -
185B ARG 3.4 5.8 - - - +
186B ASP 4.6 1.3 - - - +
187B LEU* 3.8 23.1 - - + -
190B VAL* 3.7 31.2 - - + -
215B TYR* 3.7 12.0 - - - +
216B HIS* 2.8 23.6 + - + +
218B TYR* 3.6 33.0 - - + -
220B PHE* 3.5 22.9 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il